BackgroundFermentative bacteria offer the potential to convert lignocellulosic waste-streams into biofuels such as hydrogen H2 and ethanol. Current fermentative H2 and ethanol yields, however, are below theoretical maxima, vary greatly among organisms, and depend on the extent of metabolic pathways utilized. For fermentative H2 and-or ethanol production to become practical, biofuel yields must be increased. We performed a comparative meta-analysis of i reported end-product yields, and ii genes encoding pyruvate metabolism and end-product synthesis pathways to identify suitable biomarkers for screening a microorganisms potential of H2 and-or ethanol production, and to identify targets for metabolic engineering to improve biofuel yields. Our interest in H2 and-or ethanol optimization restricted our meta-analysis to organisms with sequenced genomes and limited branched end-product pathways. These included members of the Firmicutes, Euryarchaeota, and Thermotogae.

ResultsBioinformatic analysis revealed that the absence of genes encoding acetaldehyde dehydrogenase and bifunctional acetaldehyde-alcohol dehydrogenase AdhE in Caldicellulosiruptor, Thermococcus, Pyrococcus, and Thermotoga species coincide with high H2 yields and low ethanol production. Organisms containing genes or activities for both ethanol and H2 synthesis pathways i.e. Caldanaerobacter subterraneus subsp. tengcongensis, Ethanoligenens harbinense, and Clostridium species had relatively uniform mixed product patterns. The absence of hydrogenases in Geobacillus and Bacillus species did not confer high ethanol production, but rather high lactate production. Only Thermoanaerobacter pseudethanolicus produced relatively high ethanol and low H2 yields. This may be attributed to the presence of genes encoding proteins that promote NADH production. Lactate dehydrogenase and pyruvate:formate lyase are not conducive for ethanol and-or H2 production. While the types of encoded hydrogenases appear to have little impact on H2 production in organisms that do not encode ethanol producing pathways, they do influence reduced end-product yields in those that do.

ConclusionsHere we show that composition of genes encoding pathways involved in pyruvate catabolism and end-product synthesis pathways can be used to approximate potential end-product distribution patterns. We have identified a number of genetic biomarkers for streamlining ethanol and H2 producing capabilities. By linking genome content, reaction thermodynamics, and end-product yields, we offer potential targets for optimization of either ethanol or H2 yields through metabolic engineering.

AbbreviationsACKAcetate kinase

ADHAlcohol dehydrogenase

AdhEAcetaldehyde-alcohol dehydrogenase bifunctional

AldHAldehyde dehydrogenase

ATKAcetate thiokinase

EchEnergy conserving hydrogenase

FdFerredoxin

FDPFructose-1,6-bisphosphate

FHLFormate hydrogen lyase

GAPDHGlyceraldehyde-3-phosphate dehydrogenase

GAPFORGlyceraldehydes-3-phosphate ferredoxin oxidoreductase

H2aseHydrogenase

IMGIntegrated Microbial Genomes

KOKEGG Orthology

LDHLactate dehydrogenase

MalEMalic enzyme

MbhMembrane-bound hydrogenase

MDHMalate dehydrogenase

NFONADH:ferredoxin oxidoreductase

O-ROxidation-reduction

OAADCOxaloacetate decarboxylase

PDHPyruvate dehydrogenase

PEPPhosphoenolpyruvate

PEPCKPhosphoenolpyruvate carboxykinase

PFKPhosphofructokinase

PFLPyruvate:formate lyase

PFORPyruvate:ferredoxin oxidoreductase

PGKPhosphoglycerate kinase

PPDKPyruvate phosphate dikinase

PPKPyruvate kinase

PTAPhosphotransacetylase

RnfRhodobacter nitrogen fixation

RVEPTotal molar reduction values of reduced end-products H2+ethanol.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2180-12-295 contains supplementary material, which is available to authorized users.